Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. [CODE: scripts]

This repository contains the shell, R and python scripts used to generate 4 different analyses:<br>Pre-processing: scripts responsible for generating of alignment files for downstream analyses, merging of said alignment files, generating of bigWig files for data visualisation and various Quality Control (QC)<br>Differential histone post-translational modifications (DHPTMs): scripts which estimate shift sizes and peaks from ChIP-seq data, and identify DHPTMs in peaks, transcription start site (TSS) regions and gene bodies<br>Differentially methylated regions (DMRs): scripts which identify DMRs within MeDIP-seq data<br>Differentially expressed genes (DEGs) and exons (DEEs): scripts responsible for counting number of reads in genes and exons, and determining DEGs and DEEs<br><br>The complete details on how to run the various scripts are included in the file run_scientific_data_analysis.pdf, which shows how to run all analyses with the aid of reference files (https://dx.doi.org/10.6084/m9.figshare.3487679) and demo samples (https://dx.doi.org/10.6084/m9.figshare.3487391)<br>

本仓库包含用于生成4类不同分析的Shell、R及Python脚本：
预处理（Pre-processing）：负责为下游分析生成比对文件、合并上述比对文件、生成用于数据可视化的bigWig文件，并开展各类质量控制（Quality Control, QC）工作的脚本；
组蛋白翻译后差异修饰（Differential histone post-translational modifications, DHPTMs）：用于从染色质免疫共沉淀测序（ChIP-seq）数据中估算偏移大小与峰信号，并在峰区、转录起始位点（Transcription Start Site, TSS）区域及基因本体中识别DHPTMs的脚本；
差异甲基化区域（Differentially methylated regions, DMRs）：用于在甲基化DNA免疫沉淀测序（MeDIP-seq）数据中识别DMRs的脚本；
差异表达基因（Differentially expressed genes, DEGs）与外显子（DEEs）：负责统计基因及外显子中的测序读数数量，并鉴定DEGs与DEEs的脚本。

各类脚本的完整运行说明已收录于run_scientific_data_analysis.pdf文件中，该文档演示了如何借助参考文件（https://dx.doi.org/10.6084/m9.figshare.3487679）与演示样本（https://dx.doi.org/10.6084/m9.figshare.3487391）完成全部分析流程。